Note
Click here to download the full example code
RecoBundles80 using AFQ API#
An example using the AFQ API to run recobundles with the 80 bundle atlas.
import os.path as op
import plotly
from AFQ.api.group import GroupAFQ
import AFQ.data.fetch as afd
Get some example data#
Retrieves Stanford HARDI dataset.
afd.organize_stanford_data(clear_previous_afq=True)
0%| | 0/5578 [00:00<?, ? MB/s]
0%| | 3/5578 [00:00<03:12, 28.99 MB/s]
0%| | 6/5578 [00:00<03:10, 29.20 MB/s]
0%| | 9/5578 [00:00<03:10, 29.24 MB/s]
0%| | 14/5578 [00:00<02:30, 36.96 MB/s]
0%| | 19/5578 [00:00<02:14, 41.20 MB/s]
0%| | 26/5578 [00:00<01:50, 50.47 MB/s]
1%| | 35/5578 [00:00<01:28, 62.56 MB/s]
1%| | 45/5578 [00:00<01:15, 73.65 MB/s]
1%|1 | 57/5578 [00:00<01:03, 87.26 MB/s]
1%|1 | 73/5578 [00:01<00:50, 108.69 MB/s]
2%|1 | 88/5578 [00:01<00:45, 120.41 MB/s]
2%|1 | 104/5578 [00:01<00:41, 131.16 MB/s]
2%|2 | 120/5578 [00:01<00:39, 138.80 MB/s]
2%|2 | 136/5578 [00:01<00:37, 144.12 MB/s]
3%|2 | 152/5578 [00:01<00:36, 147.74 MB/s]
3%|3 | 168/5578 [00:01<00:35, 150.38 MB/s]
3%|3 | 184/5578 [00:01<00:35, 151.89 MB/s]
4%|3 | 200/5578 [00:01<00:35, 153.05 MB/s]
4%|3 | 216/5578 [00:01<00:34, 153.88 MB/s]
4%|4 | 232/5578 [00:02<00:34, 154.48 MB/s]
4%|4 | 248/5578 [00:02<00:34, 154.44 MB/s]
5%|4 | 264/5578 [00:02<00:34, 155.29 MB/s]
5%|5 | 280/5578 [00:02<00:34, 155.49 MB/s]
5%|5 | 296/5578 [00:02<00:33, 155.69 MB/s]
6%|5 | 312/5578 [00:02<00:34, 154.54 MB/s]
6%|5 | 328/5578 [00:02<00:33, 154.80 MB/s]
6%|6 | 344/5578 [00:02<00:33, 154.93 MB/s]
6%|6 | 360/5578 [00:02<00:33, 155.05 MB/s]
7%|6 | 376/5578 [00:02<00:33, 155.33 MB/s]
7%|7 | 392/5578 [00:03<00:33, 155.60 MB/s]
7%|7 | 408/5578 [00:03<00:33, 155.94 MB/s]
8%|7 | 424/5578 [00:03<00:33, 155.96 MB/s]
8%|7 | 440/5578 [00:03<00:32, 156.14 MB/s]
8%|8 | 456/5578 [00:03<00:32, 156.08 MB/s]
8%|8 | 472/5578 [00:03<00:32, 155.72 MB/s]
9%|8 | 488/5578 [00:03<00:32, 155.78 MB/s]
9%|9 | 504/5578 [00:03<00:32, 156.06 MB/s]
9%|9 | 520/5578 [00:03<00:32, 156.15 MB/s]
10%|9 | 536/5578 [00:04<00:32, 155.96 MB/s]
10%|9 | 552/5578 [00:04<00:32, 155.71 MB/s]
10%|# | 568/5578 [00:04<00:32, 155.57 MB/s]
10%|# | 584/5578 [00:04<00:32, 155.42 MB/s]
11%|# | 600/5578 [00:04<00:31, 155.86 MB/s]
11%|#1 | 616/5578 [00:04<00:31, 155.99 MB/s]
11%|#1 | 632/5578 [00:04<00:31, 156.18 MB/s]
12%|#1 | 648/5578 [00:04<00:31, 155.94 MB/s]
12%|#1 | 664/5578 [00:04<00:31, 155.94 MB/s]
12%|#2 | 680/5578 [00:04<00:31, 155.69 MB/s]
12%|#2 | 696/5578 [00:05<00:31, 155.37 MB/s]
13%|#2 | 712/5578 [00:05<00:31, 155.52 MB/s]
13%|#3 | 728/5578 [00:05<00:31, 155.56 MB/s]
13%|#3 | 744/5578 [00:05<00:31, 155.85 MB/s]
14%|#3 | 760/5578 [00:05<00:30, 155.81 MB/s]
14%|#3 | 776/5578 [00:05<00:30, 155.58 MB/s]
14%|#4 | 792/5578 [00:05<00:30, 155.49 MB/s]
14%|#4 | 808/5578 [00:05<00:30, 155.60 MB/s]
15%|#4 | 824/5578 [00:05<00:30, 155.56 MB/s]
15%|#5 | 840/5578 [00:05<00:30, 155.48 MB/s]
15%|#5 | 856/5578 [00:06<00:30, 155.31 MB/s]
16%|#5 | 872/5578 [00:06<00:30, 155.67 MB/s]
16%|#5 | 888/5578 [00:06<00:30, 156.08 MB/s]
16%|#6 | 904/5578 [00:06<00:29, 155.84 MB/s]
16%|#6 | 920/5578 [00:06<00:29, 155.96 MB/s]
17%|#6 | 936/5578 [00:06<00:29, 156.03 MB/s]
17%|#7 | 952/5578 [00:06<00:29, 155.76 MB/s]
17%|#7 | 968/5578 [00:06<00:29, 155.44 MB/s]
18%|#7 | 984/5578 [00:06<00:29, 155.56 MB/s]
18%|#7 | 1000/5578 [00:06<00:29, 155.77 MB/s]
18%|#8 | 1016/5578 [00:07<00:29, 155.86 MB/s]
19%|#8 | 1032/5578 [00:07<00:29, 155.49 MB/s]
19%|#8 | 1048/5578 [00:07<00:29, 155.89 MB/s]
19%|#9 | 1064/5578 [00:07<00:28, 155.79 MB/s]
19%|#9 | 1080/5578 [00:07<00:28, 155.83 MB/s]
20%|#9 | 1096/5578 [00:07<00:28, 156.03 MB/s]
20%|#9 | 1112/5578 [00:07<00:28, 155.89 MB/s]
20%|## | 1128/5578 [00:07<00:28, 155.83 MB/s]
21%|## | 1144/5578 [00:07<00:28, 155.82 MB/s]
21%|## | 1160/5578 [00:08<00:31, 139.74 MB/s]
21%|##1 | 1176/5578 [00:08<00:31, 139.94 MB/s]
21%|##1 | 1192/5578 [00:08<00:30, 144.60 MB/s]
22%|##1 | 1208/5578 [00:08<00:29, 148.06 MB/s]
22%|##1 | 1224/5578 [00:08<00:28, 150.47 MB/s]
22%|##2 | 1240/5578 [00:08<00:28, 151.71 MB/s]
23%|##2 | 1256/5578 [00:08<00:28, 152.65 MB/s]
23%|##2 | 1272/5578 [00:08<00:28, 153.52 MB/s]
23%|##3 | 1288/5578 [00:08<00:28, 150.75 MB/s]
23%|##3 | 1304/5578 [00:08<00:28, 152.21 MB/s]
24%|##3 | 1320/5578 [00:09<00:27, 153.40 MB/s]
24%|##3 | 1336/5578 [00:09<00:27, 153.97 MB/s]
24%|##4 | 1352/5578 [00:09<00:27, 154.50 MB/s]
25%|##4 | 1368/5578 [00:09<00:27, 154.94 MB/s]
25%|##4 | 1384/5578 [00:09<00:27, 155.21 MB/s]
25%|##5 | 1400/5578 [00:09<00:26, 155.45 MB/s]
25%|##5 | 1416/5578 [00:09<00:26, 155.59 MB/s]
26%|##5 | 1432/5578 [00:09<00:26, 155.73 MB/s]
26%|##5 | 1448/5578 [00:09<00:26, 155.72 MB/s]
26%|##6 | 1464/5578 [00:10<00:26, 155.93 MB/s]
27%|##6 | 1480/5578 [00:10<00:26, 155.92 MB/s]
27%|##6 | 1496/5578 [00:10<00:26, 155.83 MB/s]
27%|##7 | 1512/5578 [00:10<00:26, 155.86 MB/s]
27%|##7 | 1528/5578 [00:10<00:25, 156.00 MB/s]
28%|##7 | 1544/5578 [00:10<00:25, 155.90 MB/s]
28%|##7 | 1560/5578 [00:10<00:25, 155.84 MB/s]
28%|##8 | 1576/5578 [00:10<00:25, 155.88 MB/s]
29%|##8 | 1592/5578 [00:10<00:25, 155.96 MB/s]
29%|##8 | 1608/5578 [00:10<00:25, 155.92 MB/s]
29%|##9 | 1624/5578 [00:11<00:25, 155.73 MB/s]
29%|##9 | 1640/5578 [00:11<00:25, 155.62 MB/s]
30%|##9 | 1656/5578 [00:11<00:25, 155.32 MB/s]
30%|##9 | 1672/5578 [00:11<00:25, 155.29 MB/s]
30%|### | 1688/5578 [00:11<00:25, 155.12 MB/s]
31%|### | 1704/5578 [00:11<00:24, 155.39 MB/s]
31%|### | 1720/5578 [00:11<00:24, 155.59 MB/s]
31%|###1 | 1736/5578 [00:11<00:24, 155.82 MB/s]
31%|###1 | 1752/5578 [00:11<00:24, 155.88 MB/s]
32%|###1 | 1768/5578 [00:11<00:24, 155.62 MB/s]
32%|###1 | 1784/5578 [00:12<00:24, 155.54 MB/s]
32%|###2 | 1800/5578 [00:12<00:24, 155.21 MB/s]
33%|###2 | 1816/5578 [00:12<00:24, 155.31 MB/s]
33%|###2 | 1832/5578 [00:12<00:24, 155.38 MB/s]
33%|###3 | 1848/5578 [00:12<00:24, 155.22 MB/s]
33%|###3 | 1864/5578 [00:12<00:23, 155.16 MB/s]
34%|###3 | 1880/5578 [00:12<00:23, 155.22 MB/s]
34%|###3 | 1896/5578 [00:12<00:23, 155.37 MB/s]
34%|###4 | 1912/5578 [00:12<00:23, 155.57 MB/s]
35%|###4 | 1928/5578 [00:13<00:23, 154.92 MB/s]
35%|###4 | 1944/5578 [00:13<00:23, 155.41 MB/s]
35%|###5 | 1960/5578 [00:13<00:23, 155.58 MB/s]
35%|###5 | 1976/5578 [00:13<00:23, 155.77 MB/s]
36%|###5 | 1992/5578 [00:13<00:23, 155.89 MB/s]
36%|###5 | 2008/5578 [00:13<00:22, 155.94 MB/s]
36%|###6 | 2024/5578 [00:13<00:22, 156.04 MB/s]
37%|###6 | 2040/5578 [00:13<00:22, 156.02 MB/s]
37%|###6 | 2056/5578 [00:13<00:22, 156.06 MB/s]
37%|###7 | 2072/5578 [00:13<00:22, 156.24 MB/s]
37%|###7 | 2088/5578 [00:14<00:22, 156.20 MB/s]
38%|###7 | 2104/5578 [00:14<00:22, 156.28 MB/s]
38%|###8 | 2120/5578 [00:14<00:22, 155.85 MB/s]
38%|###8 | 2136/5578 [00:14<00:22, 155.29 MB/s]
39%|###8 | 2152/5578 [00:14<00:22, 155.10 MB/s]
39%|###8 | 2168/5578 [00:14<00:21, 155.36 MB/s]
39%|###9 | 2184/5578 [00:14<00:21, 155.11 MB/s]
39%|###9 | 2200/5578 [00:14<00:21, 154.96 MB/s]
40%|###9 | 2216/5578 [00:14<00:21, 155.14 MB/s]
40%|#### | 2232/5578 [00:14<00:21, 154.93 MB/s]
40%|#### | 2248/5578 [00:15<00:21, 155.16 MB/s]
41%|#### | 2264/5578 [00:15<00:21, 155.30 MB/s]
41%|#### | 2280/5578 [00:15<00:21, 155.35 MB/s]
41%|####1 | 2296/5578 [00:15<00:21, 155.41 MB/s]
41%|####1 | 2312/5578 [00:15<00:21, 155.47 MB/s]
42%|####1 | 2328/5578 [00:15<00:20, 155.59 MB/s]
42%|####2 | 2344/5578 [00:15<00:20, 155.79 MB/s]
42%|####2 | 2360/5578 [00:15<00:20, 155.68 MB/s]
43%|####2 | 2376/5578 [00:15<00:20, 155.72 MB/s]
43%|####2 | 2392/5578 [00:15<00:20, 155.18 MB/s]
43%|####3 | 2408/5578 [00:16<00:20, 155.33 MB/s]
43%|####3 | 2424/5578 [00:16<00:20, 155.12 MB/s]
44%|####3 | 2440/5578 [00:16<00:20, 155.14 MB/s]
44%|####4 | 2456/5578 [00:16<00:20, 154.77 MB/s]
44%|####4 | 2472/5578 [00:16<00:20, 154.81 MB/s]
45%|####4 | 2488/5578 [00:16<00:19, 154.74 MB/s]
45%|####4 | 2504/5578 [00:16<00:19, 155.12 MB/s]
45%|####5 | 2520/5578 [00:16<00:19, 155.09 MB/s]
45%|####5 | 2536/5578 [00:16<00:19, 155.42 MB/s]
46%|####5 | 2552/5578 [00:17<00:19, 155.54 MB/s]
46%|####6 | 2568/5578 [00:17<00:19, 155.53 MB/s]
46%|####6 | 2584/5578 [00:17<00:19, 155.77 MB/s]
47%|####6 | 2600/5578 [00:17<00:19, 155.90 MB/s]
47%|####6 | 2616/5578 [00:17<00:19, 155.78 MB/s]
47%|####7 | 2632/5578 [00:17<00:18, 155.14 MB/s]
47%|####7 | 2648/5578 [00:17<00:18, 155.36 MB/s]
48%|####7 | 2664/5578 [00:17<00:18, 155.55 MB/s]
48%|####8 | 2680/5578 [00:17<00:18, 155.06 MB/s]
48%|####8 | 2696/5578 [00:17<00:18, 155.35 MB/s]
49%|####8 | 2712/5578 [00:18<00:18, 155.57 MB/s]
49%|####8 | 2728/5578 [00:18<00:18, 155.62 MB/s]
49%|####9 | 2744/5578 [00:18<00:18, 155.64 MB/s]
49%|####9 | 2760/5578 [00:18<00:18, 155.62 MB/s]
50%|####9 | 2776/5578 [00:18<00:18, 155.50 MB/s]
50%|##### | 2792/5578 [00:18<00:17, 155.59 MB/s]
50%|##### | 2808/5578 [00:18<00:17, 155.81 MB/s]
51%|##### | 2824/5578 [00:18<00:17, 155.47 MB/s]
51%|##### | 2840/5578 [00:18<00:17, 155.27 MB/s]
51%|#####1 | 2856/5578 [00:18<00:17, 155.52 MB/s]
51%|#####1 | 2872/5578 [00:19<00:17, 155.41 MB/s]
52%|#####1 | 2888/5578 [00:19<00:17, 155.54 MB/s]
52%|#####2 | 2904/5578 [00:19<00:17, 155.57 MB/s]
52%|#####2 | 2920/5578 [00:19<00:17, 155.78 MB/s]
53%|#####2 | 2936/5578 [00:19<00:16, 155.46 MB/s]
53%|#####2 | 2952/5578 [00:19<00:16, 155.31 MB/s]
53%|#####3 | 2968/5578 [00:19<00:16, 155.34 MB/s]
53%|#####3 | 2984/5578 [00:19<00:16, 155.40 MB/s]
54%|#####3 | 3000/5578 [00:19<00:19, 135.37 MB/s]
54%|#####4 | 3016/5578 [00:20<00:18, 140.96 MB/s]
54%|#####4 | 3032/5578 [00:20<00:17, 144.83 MB/s]
55%|#####4 | 3048/5578 [00:20<00:17, 147.95 MB/s]
55%|#####4 | 3064/5578 [00:20<00:16, 150.18 MB/s]
55%|#####5 | 3080/5578 [00:20<00:16, 151.82 MB/s]
56%|#####5 | 3096/5578 [00:20<00:16, 153.09 MB/s]
56%|#####5 | 3112/5578 [00:20<00:16, 153.93 MB/s]
56%|#####6 | 3128/5578 [00:20<00:15, 154.59 MB/s]
56%|#####6 | 3144/5578 [00:20<00:15, 155.03 MB/s]
57%|#####6 | 3160/5578 [00:20<00:15, 155.06 MB/s]
57%|#####6 | 3176/5578 [00:21<00:15, 155.26 MB/s]
57%|#####7 | 3192/5578 [00:21<00:15, 155.36 MB/s]
58%|#####7 | 3208/5578 [00:21<00:15, 155.41 MB/s]
58%|#####7 | 3224/5578 [00:21<00:15, 155.25 MB/s]
58%|#####8 | 3240/5578 [00:21<00:15, 155.33 MB/s]
58%|#####8 | 3256/5578 [00:21<00:14, 155.42 MB/s]
59%|#####8 | 3272/5578 [00:21<00:14, 155.73 MB/s]
59%|#####8 | 3288/5578 [00:21<00:14, 155.92 MB/s]
59%|#####9 | 3304/5578 [00:21<00:14, 156.11 MB/s]
60%|#####9 | 3320/5578 [00:22<00:14, 155.91 MB/s]
60%|#####9 | 3336/5578 [00:22<00:14, 155.75 MB/s]
60%|###### | 3352/5578 [00:22<00:14, 155.65 MB/s]
60%|###### | 3368/5578 [00:22<00:14, 155.84 MB/s]
61%|###### | 3384/5578 [00:22<00:14, 155.70 MB/s]
61%|###### | 3400/5578 [00:22<00:13, 155.72 MB/s]
61%|######1 | 3416/5578 [00:22<00:13, 155.72 MB/s]
62%|######1 | 3432/5578 [00:22<00:13, 155.72 MB/s]
62%|######1 | 3448/5578 [00:22<00:13, 155.88 MB/s]
62%|######2 | 3464/5578 [00:22<00:13, 155.75 MB/s]
62%|######2 | 3480/5578 [00:23<00:13, 155.78 MB/s]
63%|######2 | 3496/5578 [00:23<00:13, 155.64 MB/s]
63%|######2 | 3512/5578 [00:23<00:13, 155.51 MB/s]
63%|######3 | 3528/5578 [00:23<00:13, 155.76 MB/s]
64%|######3 | 3544/5578 [00:23<00:13, 155.67 MB/s]
64%|######3 | 3560/5578 [00:23<00:12, 155.42 MB/s]
64%|######4 | 3576/5578 [00:23<00:12, 155.37 MB/s]
64%|######4 | 3592/5578 [00:23<00:12, 155.42 MB/s]
65%|######4 | 3608/5578 [00:23<00:12, 155.44 MB/s]
65%|######4 | 3624/5578 [00:23<00:12, 155.36 MB/s]
65%|######5 | 3640/5578 [00:24<00:12, 155.48 MB/s]
66%|######5 | 3656/5578 [00:24<00:12, 155.63 MB/s]
66%|######5 | 3672/5578 [00:24<00:12, 155.50 MB/s]
66%|######6 | 3688/5578 [00:24<00:12, 155.51 MB/s]
66%|######6 | 3704/5578 [00:24<00:12, 155.81 MB/s]
67%|######6 | 3720/5578 [00:24<00:11, 155.54 MB/s]
67%|######6 | 3736/5578 [00:24<00:11, 155.78 MB/s]
67%|######7 | 3752/5578 [00:24<00:11, 155.25 MB/s]
68%|######7 | 3768/5578 [00:24<00:11, 155.13 MB/s]
68%|######7 | 3784/5578 [00:24<00:11, 155.37 MB/s]
68%|######8 | 3800/5578 [00:25<00:11, 155.67 MB/s]
68%|######8 | 3816/5578 [00:25<00:11, 155.58 MB/s]
69%|######8 | 3832/5578 [00:25<00:11, 155.72 MB/s]
69%|######8 | 3848/5578 [00:25<00:11, 155.77 MB/s]
69%|######9 | 3864/5578 [00:25<00:10, 155.89 MB/s]
70%|######9 | 3880/5578 [00:25<00:10, 155.93 MB/s]
70%|######9 | 3896/5578 [00:25<00:10, 155.75 MB/s]
70%|####### | 3912/5578 [00:25<00:10, 155.69 MB/s]
70%|####### | 3928/5578 [00:25<00:10, 155.65 MB/s]
71%|####### | 3944/5578 [00:26<00:10, 155.36 MB/s]
71%|####### | 3960/5578 [00:26<00:10, 155.72 MB/s]
71%|#######1 | 3976/5578 [00:26<00:10, 156.04 MB/s]
72%|#######1 | 3992/5578 [00:26<00:10, 155.68 MB/s]
72%|#######1 | 4008/5578 [00:26<00:10, 155.50 MB/s]
72%|#######2 | 4024/5578 [00:26<00:10, 155.23 MB/s]
72%|#######2 | 4040/5578 [00:26<00:09, 155.20 MB/s]
73%|#######2 | 4056/5578 [00:26<00:09, 155.57 MB/s]
73%|#######3 | 4072/5578 [00:26<00:09, 155.99 MB/s]
73%|#######3 | 4088/5578 [00:26<00:09, 156.00 MB/s]
74%|#######3 | 4104/5578 [00:27<00:09, 156.05 MB/s]
74%|#######3 | 4120/5578 [00:27<00:09, 155.91 MB/s]
74%|#######4 | 4136/5578 [00:27<00:09, 156.12 MB/s]
74%|#######4 | 4152/5578 [00:27<00:09, 155.56 MB/s]
75%|#######4 | 4168/5578 [00:27<00:09, 155.56 MB/s]
75%|#######5 | 4184/5578 [00:27<00:08, 155.21 MB/s]
75%|#######5 | 4200/5578 [00:27<00:08, 155.23 MB/s]
76%|#######5 | 4216/5578 [00:27<00:08, 153.00 MB/s]
76%|#######5 | 4232/5578 [00:27<00:08, 153.44 MB/s]
76%|#######6 | 4248/5578 [00:27<00:08, 153.87 MB/s]
76%|#######6 | 4264/5578 [00:28<00:08, 154.61 MB/s]
77%|#######6 | 4280/5578 [00:28<00:08, 155.09 MB/s]
77%|#######7 | 4296/5578 [00:28<00:08, 155.02 MB/s]
77%|#######7 | 4312/5578 [00:28<00:08, 155.49 MB/s]
78%|#######7 | 4328/5578 [00:28<00:08, 155.82 MB/s]
78%|#######7 | 4344/5578 [00:28<00:07, 156.02 MB/s]
78%|#######8 | 4360/5578 [00:28<00:07, 156.15 MB/s]
78%|#######8 | 4376/5578 [00:28<00:07, 156.04 MB/s]
79%|#######8 | 4392/5578 [00:28<00:07, 156.26 MB/s]
79%|#######9 | 4408/5578 [00:28<00:07, 156.21 MB/s]
79%|#######9 | 4424/5578 [00:29<00:07, 156.36 MB/s]
80%|#######9 | 4440/5578 [00:29<00:07, 155.97 MB/s]
80%|#######9 | 4456/5578 [00:29<00:07, 155.29 MB/s]
80%|######## | 4472/5578 [00:29<00:07, 155.47 MB/s]
80%|######## | 4488/5578 [00:29<00:06, 155.76 MB/s]
81%|######## | 4504/5578 [00:29<00:07, 140.38 MB/s]
81%|########1 | 4520/5578 [00:29<00:07, 144.74 MB/s]
81%|########1 | 4536/5578 [00:29<00:07, 147.74 MB/s]
82%|########1 | 4552/5578 [00:29<00:06, 150.22 MB/s]
82%|########1 | 4568/5578 [00:30<00:06, 151.97 MB/s]
82%|########2 | 4584/5578 [00:30<00:06, 147.06 MB/s]
82%|########2 | 4600/5578 [00:30<00:06, 149.50 MB/s]
83%|########2 | 4616/5578 [00:30<00:06, 151.44 MB/s]
83%|########3 | 4632/5578 [00:30<00:06, 152.71 MB/s]
83%|########3 | 4648/5578 [00:30<00:06, 153.86 MB/s]
84%|########3 | 4664/5578 [00:30<00:05, 154.43 MB/s]
84%|########3 | 4680/5578 [00:30<00:05, 154.69 MB/s]
84%|########4 | 4696/5578 [00:30<00:05, 154.97 MB/s]
84%|########4 | 4712/5578 [00:31<00:05, 155.24 MB/s]
85%|########4 | 4728/5578 [00:31<00:05, 155.52 MB/s]
85%|########5 | 4744/5578 [00:31<00:05, 155.57 MB/s]
85%|########5 | 4760/5578 [00:31<00:05, 155.47 MB/s]
86%|########5 | 4776/5578 [00:31<00:05, 155.32 MB/s]
86%|########5 | 4792/5578 [00:31<00:05, 155.13 MB/s]
86%|########6 | 4808/5578 [00:31<00:04, 155.54 MB/s]
86%|########6 | 4824/5578 [00:31<00:04, 155.87 MB/s]
87%|########6 | 4840/5578 [00:31<00:04, 155.82 MB/s]
87%|########7 | 4856/5578 [00:31<00:04, 155.32 MB/s]
87%|########7 | 4872/5578 [00:32<00:04, 155.46 MB/s]
88%|########7 | 4888/5578 [00:32<00:04, 155.31 MB/s]
88%|########7 | 4904/5578 [00:32<00:04, 155.41 MB/s]
88%|########8 | 4920/5578 [00:32<00:04, 155.32 MB/s]
88%|########8 | 4936/5578 [00:32<00:04, 155.92 MB/s]
89%|########8 | 4952/5578 [00:32<00:04, 156.10 MB/s]
89%|########9 | 4968/5578 [00:32<00:03, 156.03 MB/s]
89%|########9 | 4984/5578 [00:32<00:03, 155.95 MB/s]
90%|########9 | 5000/5578 [00:32<00:03, 156.17 MB/s]
90%|########9 | 5016/5578 [00:32<00:03, 156.19 MB/s]
90%|######### | 5032/5578 [00:33<00:03, 156.30 MB/s]
90%|######### | 5048/5578 [00:33<00:03, 156.55 MB/s]
91%|######### | 5064/5578 [00:33<00:03, 156.46 MB/s]
91%|#########1| 5080/5578 [00:33<00:03, 156.01 MB/s]
91%|#########1| 5096/5578 [00:33<00:03, 156.17 MB/s]
92%|#########1| 5112/5578 [00:33<00:02, 155.95 MB/s]
92%|#########1| 5128/5578 [00:33<00:02, 155.77 MB/s]
92%|#########2| 5144/5578 [00:33<00:02, 155.52 MB/s]
93%|#########2| 5160/5578 [00:33<00:02, 155.68 MB/s]
93%|#########2| 5176/5578 [00:33<00:02, 156.00 MB/s]
93%|#########3| 5192/5578 [00:34<00:02, 155.97 MB/s]
93%|#########3| 5208/5578 [00:34<00:02, 155.19 MB/s]
94%|#########3| 5224/5578 [00:34<00:02, 155.50 MB/s]
94%|#########3| 5240/5578 [00:34<00:02, 155.51 MB/s]
94%|#########4| 5256/5578 [00:34<00:02, 155.74 MB/s]
95%|#########4| 5272/5578 [00:34<00:01, 155.80 MB/s]
95%|#########4| 5288/5578 [00:34<00:01, 155.94 MB/s]
95%|#########5| 5304/5578 [00:34<00:01, 155.93 MB/s]
95%|#########5| 5320/5578 [00:34<00:01, 155.89 MB/s]
96%|#########5| 5336/5578 [00:35<00:01, 156.09 MB/s]
96%|#########5| 5352/5578 [00:35<00:01, 155.98 MB/s]
96%|#########6| 5368/5578 [00:35<00:01, 155.71 MB/s]
97%|#########6| 5384/5578 [00:35<00:01, 154.77 MB/s]
97%|#########6| 5400/5578 [00:35<00:01, 155.09 MB/s]
97%|#########7| 5416/5578 [00:35<00:01, 154.87 MB/s]
97%|#########7| 5432/5578 [00:35<00:00, 154.89 MB/s]
98%|#########7| 5448/5578 [00:35<00:00, 155.08 MB/s]
98%|#########7| 5464/5578 [00:35<00:00, 155.47 MB/s]
98%|#########8| 5480/5578 [00:35<00:00, 155.63 MB/s]
99%|#########8| 5496/5578 [00:36<00:00, 155.75 MB/s]
99%|#########8| 5512/5578 [00:36<00:00, 155.98 MB/s]
99%|#########9| 5528/5578 [00:36<00:00, 156.06 MB/s]
99%|#########9| 5544/5578 [00:36<00:00, 156.27 MB/s]
100%|#########9| 5560/5578 [00:36<00:00, 156.10 MB/s]
100%|#########9| 5576/5578 [00:36<00:00, 155.93 MB/s]
100%|##########| 5578/5578 [00:36<00:00, 152.62 MB/s]
0%| | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 3223.91 MB/s]
0%| | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 2357.68 MB/s]
0%| | 0/71 [00:00<?, ? MB/s]
4%|4 | 3/71 [00:00<00:02, 28.74 MB/s]
8%|8 | 6/71 [00:00<00:02, 29.07 MB/s]
13%|#2 | 9/71 [00:00<00:02, 29.17 MB/s]
20%|#9 | 14/71 [00:00<00:01, 36.95 MB/s]
28%|##8 | 20/71 [00:00<00:01, 44.69 MB/s]
39%|###9 | 28/71 [00:00<00:00, 55.99 MB/s]
54%|#####3 | 38/71 [00:00<00:00, 69.49 MB/s]
70%|####### | 50/71 [00:00<00:00, 84.72 MB/s]
92%|#########1| 65/71 [00:00<00:00, 104.08 MB/s]
100%|##########| 71/71 [00:00<00:00, 76.75 MB/s]
0%| | 0/4 [00:00<?, ? MB/s]
100%|##########| 4/4 [00:00<00:00, 1718.27 MB/s]
0%| | 0/1 [00:00<?, ? MB/s]
100%|##########| 1/1 [00:00<00:00, 2563.76 MB/s]
Set tractography parameters (optional)#
We make this tracking_params which we will pass to the GroupAFQ object which specifies that we want 50,000 seeds randomly distributed in the white matter.
We only do this to make this example faster and consume less space.
tracking_params = dict(n_seeds=50000,
random_seeds=True,
rng_seed=42)
Initialize a GroupAFQ object:#
We specify seg_algo as reco80 in segmentation_params. This tells the AFQ object to perform RecoBundles using the 80 bundles atlas in the segmentation step.
myafq = GroupAFQ(bids_path=op.join(afd.afq_home,
'stanford_hardi'),
preproc_pipeline='vistasoft',
segmentation_params={"seg_algo": "reco80"},
tracking_params=tracking_params)
/opt/hostedtoolcache/Python/3.9.16/x64/lib/python3.9/site-packages/bids/layout/validation.py:156: UserWarning:
The PipelineDescription field was superseded by GeneratedBy in BIDS 1.4.0. You can use ``pybids upgrade`` to update your derivative dataset.
Visualizing bundles and tract profiles:#
This would run the script and visualize the bundles using the plotly interactive visualization, which should automatically open in a new browser window.
bundle_html = myafq.export("all_bundles_figure")
plotly.io.show(bundle_html["01"][0])